Analytical Sciences

Spectroscopic Analyses of the Noncovalent Self-Assembly of Cyanines upon Various Nucleic Acid Scaffolds

Komandoor E. ACHYUTHAN,* Jaime L. McCLAIN,* Zhijun ZHOU,** David G. WHITTEN,** and Darren W. BRANCH*

*Biosensors and Nanomaterials Department, Sandia National Laboratories, Albuquerque, NM, USA
**Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM, USA

We utilized self-assembly of cyanine chromophores to study the conformational changes in various types of nucleic acid scaffolds: single and double stranded DNA, linear or circular DNA and RNA. We identified a chromophore that became highly fluorescent after aggregating upon nucleic acids. Fluorescence from the aggregate was instantaneous after self-assembly. Temporal emission profiles displayed a biphasic trend demonstrating kinetic dependence for assembly and disassembly. Absorption spectra of the aggregate showed a red-shifted “shoulder” peak indicative of J-aggregate. Fluorescence from J-aggregates was also red-shifted. We utilized cyanine self-assembly to quantize various nucleic acids. The limits of detection and quantization for φX174 DNA were 3 and 9 fmol, respectively. We similarly determined the sensitivity for various nucleic acids and established the optimum conditions for self-assembly. Collectively, the effects of methanol, salt, and full width at half maximum for cyanine fluorescence on DNA or carboxymethylamylose scaffolds, all suggested noncovalent, electrostatic, and hydrophobic forces were involved in supramolecular self-assembly. Our results facilitate a better understanding of supramolecular self-assembly.

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